Published November 30, 2017
| Version v1
Journal article
Restricted
Discovery of a rich gene pool of bat SARSrelated coronaviruses provides new insights into the origin of SARS coronavirus
Description
Hu, Ben, Zeng, Lei-Ping, Yang, Xing-Lou, Ge, Xing-Yi, Zhang, Wei, Li, Bei, Shen, Xu-Rui, Zhang, Yun-Zhi, Wang, Ning, Luo, Dong-Sheng, Zheng, Xiao- Shuang, Wang, Mei-Niang, Daszak, Peter, Wang, Lin-Fa, Cui, Jie, Shi, Zheng- Li (2017): Discovery of a rich gene pool of bat SARSrelated coronaviruses provides new insights into the origin of SARS coronavirus. PLoS Pathogens 13 (11), No. 1006698: 1-27, DOI: 10.1371/journal.ppat.1006698
Files
Restricted
The record is publicly accessible, but files are restricted to users with access.
Linked records
Additional details
Identifiers
- LSID
- urn:lsid:plazi.org:pub:FFB5C739FFDBFFC92C10FFEEFE48FF8C
References
- 1. Peiris JS, Guan Y, Yuen KY. Severe acute respiratory syndrome.Nat Med. 2004; 10: S88-97. https:// doi.org/10.1038/nm1143 PMID: 15577937
- 2. Zhong NS, Zheng BJ, Li YM, Poon, Xie ZH, Chan KH, et al. Epidemiology and cause of severe acute respiratory syndrome (SARS) in Guangdong, People's Republic of China, in February, 2003. Lancet. 2003; 362: 1353-1358. PMID: 14585636
- 3. Chinese SMEC. Molecular evolution of the SARS coronavirus during the course of the SARS epidemic in China. Science. 2004; 303: 1666-1669.https://doi.org/10.1126/science.1092002 PMID: 14752165
- 4. Drexler JF, Corman VM, Drosten C. Ecology, evolution and classification of bat coronaviruses in the aftermath of SARS. Antiviral Res. 2014; 101: 45-56. https://doi.org/10.1016/j.antiviral.2013.10.013 PMID: 24184128
- 5. Marra MA, Jones SJ, Astell CR, Holt RA, Brooks-Wilson A, Butterfield YS, et al. The Genome sequence of the SARS-associated coronavirus. Science. 2003; 300: 1399-1404. https://doi.org/10.1126/science. 1085953 PMID: 12730501
- 6. Snijder EJ, Bredenbeek PJ, Dobbe JC, Thiel V, Ziebuhr J, Poon LL, et al. Unique and conserved features of genome and proteome of SARS-coronavirus, an early split-off from the coronavirus group 2 lineage. J Mol Biol. 2003; 331: 991-1004. PMID: 12927536
- 7. Guan Y, Zheng BJ, He YQ, Liu XL, Zhuang ZX, Cheung CL, et al. Isolation and characterization of viruses related to the SARS coronavirus from animals in southern China. Science.2003; 302: 276- 278. https://doi.org/10.1126/science.1087139 PMID: 12958366
- 8. Song HD, Tu CC, Zhang GW, Wang SY, Zheng K, Lei LC, et al. Cross-host evolution of severe acute respiratory syndrome coronavirus in palm civet and human. Proc Natl Acad Sci U S A. 2005; 102: 2430-2435. https://doi.org/10.1073/pnas.0409608102 PMID: 15695582
- 9. Li W, Shi Z, Yu M, Ren W, Smith C, Epstein JH, et al. Bats are natural reservoirs of SARS-like coronaviruses.Science. 2005; 310: 676-679. https://doi.org/10.1126/science.1118391 PMID: 16195424
- 10. Lau SK, Woo PC, Li KS, Huang Y, Tsoi HW, Wong BH, et al. Severe acute respiratory syndrome coronavirus-like virus in Chinese horseshoe bats. Proc Natl Acad Sci U S A. 2005; 102: 14040-14045. https://doi.org/10.1073/pnas.0506735102 PMID: 16169905
- 11. Tang XC, Zhang JX, Zhang SY, Wang P, Fan XH, Li LF, et al. Prevalence and genetic diversity of coronaviruses in bats from China. J Virol. 2006; 80: 7481-7490. https://doi.org/10.1128/JVI.00697-06 PMID: 16840328
- 12. Yuan J, Hon CC, Li Y, Wang D, Xu G, Zhang H, et al. Intraspecies diversity of SARS-like coronaviruses in Rhinolophus sinicus and its implications for the origin of SARS coronaviruses in humans. J Gen Virol. 2010; 91: 1058-1062. https://doi.org/10.1099/vir.0.016378-0 PMID: 20016037
- 13. He B, Zhang Y, Xu L, Yang W, Yang F, Feng Y, et al. Identification of diverse alphacoronaviruses and genomic characterization of a novel severe acute respiratory syndrome-like coronavirus from bats in China. J Virol. 2014; 88: 7070-7082. https://doi.org/10.1128/JVI.00631-14 PMID: 24719429
- 14. Wu Z, Yang L, Ren X, He G, Zhang J, Yang J, et al. Deciphering the bat virome catalog to better understand the ecological diversity of bat viruses and the bat origin of emerging infectious diseases. ISME J. 2016; 10: 609-620. https://doi.org/10.1038/ismej.2015.138 PMID: 26262818
- 15. Drexler JF, Gloza-Rausch F, Glende J, Corman VM, Muth D, Goettsche M, et al. Genomic characterization of severe acute respiratory syndrome-related coronavirus in European bats and classification of coronaviruses based on partial RNA-dependent RNA polymerase gene sequences.J Virol. 2010; 84: 11336-11349. https://doi.org/10.1128/JVI.00650-10 PMID: 20686038
- 16. Tong S, Conrardy C, Ruone S, Kuzmin IV, Guo X, Tao Y, et al. Detection of novel SARS-like and other coronaviruses in bats from Kenya. Emerg Infect Dis. 2009; 15: 482-485. https://doi.org/10.3201/ eid1503.081013 PMID: 19239771
- 17. Ge XY, Li JL, Yang XL, Chmura AA, Zhu G, Epstein JH, et al. Isolation and characterization of a bat SARS-like coronavirus that uses the ACE2 receptor. Nature. 2013; 503: 535-538. https://doi.org/10. 1038/nature12711 PMID: 24172901
- 18. Yang XL, Hu B, Wang B, Wang MN, Zhang Q, Zhang W, et al. Isolation and Characterization of a Novel Bat Coronavirus Closely Related to the Direct Progenitor of Severe Acute Respiratory Syndrome Coronavirus. J Virol. 2016; 90: 3253-3256.
- 19. Menachery VD, Yount BL Jr., Sims AC, Debbink K, Agnihothram SS, Gralinski LE, et al. SARS-like WIV1-CoV poised for human emergence. Proc Natl Acad Sci U S A. 2016; 113: 3048-3053. https://doi. org/10.1073/pnas.1517719113 PMID: 26976607
- 20. de Souza Luna LK, Heiser V, Regamey N, Panning M, Drexler JF, Mulangu S, et al. Generic detection of coronaviruses and differentiation at the prototype strain level by reverse transcription-PCR and nonfluorescent low-density microarray. J Clin Microbiol. 2007; 45: 1049-1052. https://doi.org/10.1128/ JCM.02426-06 PMID: 17229859
- 21. Ren W, Li W, Yu M, Hao P, Zhang Y, Zhou P, et al. Full-length genome sequences of two SARS-like coronaviruses in horseshoe bats and genetic variation analysis. J Gen Virol. 2006; 87: 3355-3359. https://doi.org/10.1099/vir.0.82220-0 PMID: 17030870
- 22. Lau SK, Feng Y, Chen H, Luk HK, Yang WH, Li KS, et al. Severe Acute Respiratory Syndrome (SARS) Coronavirus ORF8 Protein Is Acquired from SARS-Related Coronavirus from Greater Horseshoe Bats through Recombination. J Virol. 2015; 89: 10532-10547. https://doi.org/10.1128/JVI.01048-15 PMID: 26269185
- 23. Zeng LP, Gao YT, Ge XY, Zhang Q, Peng C, Yang XL, et al. Bat Severe Acute Respiratory Syndrome- Like Coronavirus WIV1 Encodes an Extra Accessory Protein, ORFX, Involved in Modulation of the Host Immune Response. J Virol. 2016; 90: 6573-6582. https://doi.org/10.1128/JVI.03079-15 PMID: 27170748
- 24. Li F. Evidence for a common evolutionary origin of coronavirus spike protein receptor-binding subunits. J Virol. 2012; 86: 2856-2858. https://doi.org/10.1128/JVI.06882-11 PMID: 22205743
- 25. Lau SK, Li KS, Huang Y, Shek CT, Tse H, Wang M, et al. Ecoepidemiology and complete genome comparison of different strains of severe acute respiratory syndrome-related Rhinolophus bat coronavirus in China reveal bats as a reservoir for acute, self-limiting infection that allows recombination events. J Virol. 2010; 84: 2808-2819. https://doi.org/10.1128/JVI.02219-09 PMID: 20071579
- 26. Oostra M, de Haan CA, Rottier PJ. The 29-nucleotide deletion present in human but not in animal severe acute respiratory syndrome coronaviruses disrupts the functional expression of open reading frame 8. J Virol. 2007; 81: 13876-13888. https://doi.org/10.1128/JVI.01631-07 PMID: 17928347
- 27. Kopecky-Bromberg SA, Martinez-Sobrido L, Frieman M, Baric RA, Palese P. Severe acute respiratory syndrome coronavirus open reading frame (ORF) 3b, ORF 6, and nucleocapsid proteins function as interferon antagonists. J Virol. 2007; 81: 548-557. https://doi.org/10.1128/JVI.01782-06 PMID: 17108024
- 28. Chen CY, Ping YH, Lee HC, Chen KH, Lee YM, Chen YJ, et al. Open reading frame 8a of the human severe acute respiratory syndrome coronavirus not only promotes viral replication but also induces apoptosis. J Infect Dis. 2007; 196: 405-415. https://doi.org/10.1086/519166 PMID: 17597455
- 29. Yang L, Wu Z, Ren X, Yang F, He G, Zhang J, et al. Novel SARS-like betacoronaviruses in bats, China, 2011. Emerg Infect Dis. 2013; 19: 989-991. https://doi.org/10.3201/eid1906.121648 PMID: 23739658
- 30. Wu Z, Yang L, Ren X, Zhang J, Yang F, Zhang S, et al. ORF8-Related Genetic Evidence for Chinese Horseshoe Bats as the Source of Human Severe Acute Respiratory Syndrome Coronavirus. J Infect Dis. 2016; 213: 579-583. https://doi.org/10.1093/infdis/jiv476 PMID: 26433221
- 31. Drexler JF, Corman VM, Wegner T, Tateno AF, Zerbinati RM, Gloza-Rausch F, et al. Amplification of emerging viruses in a bat colony. Emerg Infect Dis. 2011; 17: 449-456. https://doi.org/10.3201/ eid1703.100526 PMID: 21392436
- 32. Wang MN, Zhang W, Gao YT, Hu B, Ge XY, Yang XL, et al. Longitudinal surveillance of SARS-like coronaviruses in bats by quantitative real-time PCR. Virol Sin. 2016; 31: 78-80. https://doi.org/10.1007/ s12250-015-3703-3 PMID: 26920711
- 33. Menachery VD, Yount BL Jr., Debbink K, Agnihothram S, Gralinski LE, Plante JA, et al. A SARS-like cluster of circulating bat coronaviruses shows potential for human emergence. Nat Med. 2015; 21: 1508-1513. https://doi.org/10.1038/nm.3985 PMID: 26552008
- 34. Ren W, Qu X, Li W, Han Z, Yu M, Zhou P, et al. Difference in receptor usage between severe acute respiratory syndrome (SARS) coronavirus and SARS-like coronavirus of bat origin. J Virol. 2008; 82: 1899-1907. https://doi.org/10.1128/JVI.01085-07 PMID: 18077725
- 35. Sung SC, Chao CY, Jeng KS, Yang JY, Lai MM. The 8ab protein of SARS-CoV is a luminal ER membrane-associated protein and induces the activation of ATF6. Virology. 2009; 387: 402-413. https://doi. org/10.1016/j.virol.2009.02.021 PMID: 19304306
- 36. Freundt EC, Yu L, Park E, Lenardo MJ, Xu XN. Molecular determinants for subcellular localization of the severe acute respiratory syndrome coronavirus open reading frame 3b protein. J Virol. 2009; 83: 6631-6640. https://doi.org/10.1128/JVI.00367-09 PMID: 19403678
- 37. Zhou P, Li H, Wang H, Wang LF, Shi Z. Bat severe acute respiratory syndrome-like coronavirus ORF3b homologues display different interferon antagonist activities. J Gen Virol. 2012; 93: 275-281. https:// doi.org/10.1099/vir.0.033589-0 PMID: 22012463
- 38. Irwin DM, Kocher TD, Wilson AC. Evolution of the cytochrome b gene of mammals. J Mol Evol. 1991; 32: 128-144.PMID: 1901092
- 39. Mayer F, von Helversen O. Cryptic diversity in European bats. Proc Biol Sci. 2001; 268: 1825-1832. https://doi.org/10.1098/rspb.2001.1744 PMID: 11522202
- 40. Hall BG. Building phylogenetic trees from molecular data with MEGA. Mol Biol Evol. 2013; 30: 1229- 1235. https://doi.org/10.1093/molbev/mst012 PMID: 23486614
- 41. Martin DP, Lemey P, Lott M, Moulton V, Posada D, Lefeuvre P. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics. 2010; 26: 2462-2463. https://doi.org/10.1093/ bioinformatics/btq467 PMID: 20798170
- 42. Lole KS, Bollinger RC, Paranjape RS, Gadkari D, Kulkarni SS, Novak NG, et al. Full-length human immunodeficiency virus type 1 genomes from subtype C-infected seroconverters in India, with evidence of intersubtype recombination. J Virol. 1999; 73: 152-160. PMID: 9847317
- 43. Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010; 59: 307-321.https://doi.org/10.1093/sysbio/syq010 PMID: 20525638